gemmi-protools 0.1.5__py3-none-any.whl → 0.1.7__py3-none-any.whl

gemmi_protools/io/parser.py

@@ -134,14 +134,19 @@ def pdb_parser(path: Union[str, pathlib.Path]):
         block = struct.make_mmcif_block()
         ent_t = _cif_entity_info(block)
         rec = defaultdict(list)
+
         for cn, middle_eid in ent_t.polymer2eid.items():
             rec[middle_eid].append(cn)
 
         _mapper = _assign_digital_entity_names(struct)
         _mapper_n = dict()
+
         for middle_eid, new_eid in _mapper.items():
-            old_eid = str(",".join(rec[middle_eid]))
-            _mapper_n[old_eid] = new_eid
+            if middle_eid in rec:
+                mid = rec[middle_eid]
+                mid.sort()
+                old_eid = str(",".join(mid))
+                _mapper_n[old_eid] = new_eid
 
         if _mapper_n:
             _update_entity_names(ent_0, _mapper_n)

gemmi_protools/io/pdb_opts.py

@@ -119,6 +119,8 @@ def _compound_source_string(entity: Entity) -> List[str]:
         entity2polymer[v].append(k)
     entity_labels = list(entity2polymer.keys())
     entity_labels.sort()
+    for v in entity2polymer.values():
+        v.sort()
 
     values = []
     for i, el in enumerate(entity_labels):
@@ -136,9 +138,9 @@ def _compound_source_string(entity: Entity) -> List[str]:
     compound_molecule = "COMPND {n_line:>3} MOLECULE: {molecule};"
     compound_chain = "COMPND {n_line:>3} CHAIN: {chain};"
 
-    i = 0
+    i = 1
     for val in values:
-        if i == 0:
+        if i == 1:
             outputs.append(compound_mol0.format(**val))
             i += 1
             for c_str in [compound_molecule, compound_chain]:

gemmi_protools/utils/fixer.py

@@ -50,7 +50,9 @@ def clean_structure(input_file: Union[str, pathlib.Path],
                     add_missing_atoms: str = "heavy",
                     keep_heterogens: str = "all",
                     replace_nonstandard: bool = True,
-                    ph: Union[float, int] = 7.0
+                    ph: Union[float, int] = 7.0,
+                    check_mode: bool = True,
+                    threshold: float = 0.3,
                     ):
     """
 
@@ -69,6 +71,9 @@ def clean_structure(input_file: Union[str, pathlib.Path],
             none: remove all heterogens
     :param replace_nonstandard: default True, replace all non-standard residues to standard ones
     :param ph: default 7.0, ph values to add missing hydrogen atoms
+    :param check_mode: default True to check the ratio of residues with missing atoms
+    :param threshold: float, default 0.3, only use when check_mode=True
+
     :return:
         str, status message of fixing
         if successful, return Finish, otherwise message of error
@@ -82,6 +87,15 @@ def clean_structure(input_file: Union[str, pathlib.Path],
         ######################################################
         fixer = _load_by_pbdfixer(input_file)
 
+        ######################################################
+        # check
+        ######################################################
+        fixer.findMissingResidues()
+        fixer.findMissingAtoms()
+        ratio = len(fixer.missingAtoms) / fixer.topology.getNumResidues()
+        if ratio > threshold:
+            return dict(input=input_file, msg="Too many residues with missing atoms: %.2f" % ratio)
+
         ######################################################
         # replace non-standard residues
         ######################################################

{gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.5
+Version: 0.1.7
 Summary: An Enhanced tool to process PDB structures based on Gemmi
 Author-email: Luo Jiejian <luojiejian12@mails.ucas.ac.cn>
 License-Expression: MIT

{gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.7.dist-info}/RECORD

@@ -3,18 +3,18 @@ gemmi_protools/io/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E
 gemmi_protools/io/cif_opts.py,sha256=TKND91aRGB5hYNdTFElCKMGabCg4klLk_c1evC3WZuA,6368
 gemmi_protools/io/convert.py,sha256=780sQcwhslUD4Hj5UZMVlQdbicniJ6jNjncTl_7jaMk,3841
 gemmi_protools/io/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpDh_RPOicI,14223
-gemmi_protools/io/parser.py,sha256=lCeIzEnBhTl0AQPwa68PNrvj1d4vJdS99Mj-WypCvYo,9033
-gemmi_protools/io/pdb_opts.py,sha256=VYIUsEGiFtbcK2eEUi4rsRKDCfMiV-WSXzz4zivxm7A,5686
+gemmi_protools/io/parser.py,sha256=NCLc9IHH-tb2hIm0jZeKu2nVw2Isr-n-pH4l7JbKA5w,9130
+gemmi_protools/io/pdb_opts.py,sha256=laUqxlecOe6goax12q8EJGZuZbHyIGsXVucMV3gVrgg,5741
 gemmi_protools/io/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
 gemmi_protools/io/reader.py,sha256=oaJ5TTWLFCZ3tDq3R5dAyBqm4Q2sxmfl4D8cGvSOdl0,16060
 gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
 gemmi_protools/utils/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
 gemmi_protools/utils/align.py,sha256=CZcrvjy-ZbX2u7OAn-YGblbxaj9YFUDX4CFZcpbpnB8,6959
 gemmi_protools/utils/dockq.py,sha256=XmMwVEy-H4p6sH_HPcDWA3TP77OWdih0fE_BQJDr4pU,4189
-gemmi_protools/utils/fixer.py,sha256=f1MAeYkFukijaBwTdINO0733Qbe5B9xSgRCE69nHkN4,8396
+gemmi_protools/utils/fixer.py,sha256=WUiIoK8dFPGUkXlK-wiiWyorYD8T71rN7WDE2psGSiE,9061
 gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
-gemmi_protools-0.1.5.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.5.dist-info/METADATA,sha256=0IypVyv4jYIvts3I3uoQC5R_6dG8dooo1B7XC9MgavQ,567
-gemmi_protools-0.1.5.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
-gemmi_protools-0.1.5.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.5.dist-info/RECORD,,
+gemmi_protools-0.1.7.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.7.dist-info/METADATA,sha256=tsp4fzE0T7lTsmPaRYK5UzgqS4OjrvOSfESFMqbkk0Y,567
+gemmi_protools-0.1.7.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+gemmi_protools-0.1.7.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.7.dist-info/RECORD,,

{gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.1)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any